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@jvhagey jvhagey released this 22 Mar 15:43
· 832 commits to main since this release
v1.1.1
f5b1ca8
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Learn about vigilant mode.

Implemented Enhancements:

  • -entry CDC_PHOENIX workflow checks all FASTQ files for corruption and creates a list of the checked files usng the FAIry (FASTQ file Assesment of Integrity) tool commit 1111df8. This is a required internal QC check.
  • Expanded MLST lookup of Citrobacter species complex commit 43ea24d lists the new species.
  • Increased SPAdes CPUs to 8 and memory to 16GB in base.config.

Fixed Bugs:

  • Fix for issue #99 where first gene in ar, plasmid and hypervirulence genes didn't end up in the *_summaryline.tsv. This same error was in Phoenix_summary_line.py that caused the first sample to not be include in the final report.
  • Fixed tabulation error into *_combined.tsv output files that in some cases would show in GRiPHin_Report.xlsx output as a long singular line as the MLST type.
  • Fix for issue #91 where Klebsiella MLST lookup would not properly match to the correct lookup database.
  • Fixed problem where samples that didn't create scaffolds, but created contigs didn't have species printed out in Phoenix_Output_Report.tsv details in commit c7f7ea5.
  • Fixed problem in -entry CDC_PHOENIX where samples that didn't create scaffolds, but created contigs or samples that failed spades completely didn't have correct columns lining up in Phoenix_Output_Report.tsv details in commit d17bdda.
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